Add release/devel cycle and Bioc version in tag

.github/workflows/build_ghcr.yaml

@@ -16,6 +16,7 @@ jobs:
       matrix:
         ubuntu: [jammy]
         platform: [linux/amd64]
+        cycle: [devel, release]
 
     name: Build container images for GHCR
     runs-on: ubuntu-latest
@@ -62,6 +63,7 @@ jobs:
         id: build
         uses: docker/build-push-action@v4
         with:
+          build-args: CYCLE=${{matrix.cycle}}
           labels: ${{ steps.meta.outputs.labels }}
           outputs: type=image,name=${{ steps.vars.outputs.container }},push-by-digest=true,name-canonical=true,push=true
           platforms: ${{matrix.platform}}
@@ -73,7 +75,7 @@ jobs:
           cat << "EOF" > ${{matrix.ubuntu}}-${{matrix.platform}}-r.Dockerfile
           FROM ${{ steps.vars.outputs.container }}@${{ steps.build.outputs.digest }} as extract
           USER root
-          RUN mkdir /bioctmp && /bbs_r_start --version > /bioctmp/rver && cat /etc/os-release > /bioctmp/os-release
+          RUN mkdir /bioctmp && /bbs_r_start -e 'BiocManager::version()' | grep '\[1\]' | awk -F"'" '{print $2}' > /bioctmp/biocver && /bbs_r_start --version > /bioctmp/rver && cat /etc/os-release > /bioctmp/os-release
           FROM scratch as export
           COPY --from=extract /bioctmp/* /
           EOF
@@ -96,19 +98,24 @@ jobs:
           cd ${{matrix.ubuntu}}-${{matrix.platform}}
           tar -xvf r.tar
           echo rver=$(cat rver | awk 'NR==1{print $3}') >> $GITHUB_OUTPUT
+          echo biocver=$(cat biocver) >> $GITHUB_OUTPUT
           echo osver=$(awk -F= '/VERSION_ID/ {gsub("\"", "", $2); print $2}' os-release) >> $GITHUB_OUTPUT
 
       - name: Export digest by ubuntu and r versions
         run: |
           digest="${{ steps.build.outputs.digest }}"
           mkdir -p /tmp/digests/${{matrix.ubuntu}}
           touch "/tmp/digests/${{matrix.ubuntu}}/${digest#sha256:}"
-          mkdir -p /tmp/digests/${{matrix.ubuntu}}-r-${{steps.versions.outputs.rver}}
-          touch "/tmp/digests/${{matrix.ubuntu}}-r-${{steps.versions.outputs.rver}}/${digest#sha256:}"
+          mkdir -p /tmp/digests/${{matrix.ubuntu}}-bioc-${{steps.versions.outputs.biocver}}
+          touch "/tmp/digests/${{matrix.ubuntu}}-bioc-${{steps.versions.outputs.biocver}}/${digest#sha256:}"
+          mkdir -p /tmp/digests/${{matrix.ubuntu}}-bioc-${{steps.versions.outputs.biocver}}-r-${{steps.versions.outputs.rver}}
+          touch "/tmp/digests/${{matrix.ubuntu}}-bioc-${{steps.versions.outputs.biocver}}-r-${{steps.versions.outputs.rver}}/${digest#sha256:}"
           mkdir -p /tmp/digests/${{steps.versions.outputs.osver}}
           touch "/tmp/digests/${{steps.versions.outputs.osver}}/${digest#sha256:}"
-          mkdir -p /tmp/digests/${{steps.versions.outputs.osver}}-r-${{steps.versions.outputs.rver}}
-          touch "/tmp/digests/${{steps.versions.outputs.osver}}-r-${{steps.versions.outputs.rver}}/${digest#sha256:}"
+          mkdir -p /tmp/digests/${{steps.versions.outputs.osver}}-bioc-${{steps.versions.outputs.biocver}}
+          touch "/tmp/digests/${{steps.versions.outputs.osver}}-bioc-${{steps.versions.outputs.biocver}}/${digest#sha256:}"
+          mkdir -p /tmp/digests/${{steps.versions.outputs.osver}}-bioc-${{steps.versions.outputs.biocver}}-r-${{steps.versions.outputs.rver}}
+          touch "/tmp/digests/${{steps.versions.outputs.osver}}-bioc-${{steps.versions.outputs.biocver}}-r-${{steps.versions.outputs.rver}}/${digest#sha256:}"
 
       - name: Upload digests
         uses: actions/upload-artifact@v3

Dockerfile

@@ -1,8 +1,9 @@
 FROM ubuntu:jammy
+ARG CYCLE=release
 RUN useradd -ms /bin/bash biocbuild && apt update -qq && apt install sudo systemd -y && usermod -aG sudo biocbuild && echo "biocbuild ALL=(ALL) NOPASSWD:ALL" >> /etc/sudoers
 USER biocbuild
 COPY . /home/biocbuild/bioconductor_salt
 WORKDIR /home/biocbuild
-RUN bash bioconductor_salt/simple_start_linux.sh
+RUN bash bioconductor_salt/startup_bbs_standalone_${CYCLE}.sh
 ENTRYPOINT ["/bbs_r_start"]
 

simple_start_linux.sh → startup_bbs_standalone_devel.sh

@@ -25,7 +25,7 @@ sudo cp -r bioconductor_salt/saltstack/salt /srv
 sudo cp -r bioconductor_salt/saltstack/pillar /srv
 sudo cp bioconductor_salt/saltstack/minion.d/minion.conf /etc/salt/minion
 
-sudo mv /srv/pillar/custom/standalone.sls /srv/pillar/custom/init.sls
+sudo mv /srv/pillar/custom/devel_standalone.sls /srv/pillar/custom/init.sls
 
 sudo salt-call --local state.highstate -l debug || true
 

startup_bbs_standalone_release.sh

@@ -0,0 +1,51 @@
+#!/usr/bin/env bash
+
+# Basic deps
+sudo apt update -qq
+sudo apt -y install curl git build-essential python3 python3-pip locales wget
+
+# Set up saltstack
+
+# https://docs.saltproject.io/salt/install-guide/en/latest/topics/install-by-operating-system/ubuntu.html
+
+sudo curl -fsSL -o /etc/apt/keyrings/salt-archive-keyring-2023.gpg https://repo.saltproject.io/salt/py3/ubuntu/22.04/amd64/SALT-PROJECT-GPG-PUBKEY-2023.gpg
+echo "deb [signed-by=/etc/apt/keyrings/salt-archive-keyring-2023.gpg arch=amd64] https://repo.saltproject.io/salt/py3/ubuntu/22.04/amd64/latest jammy main" | sudo tee /etc/apt/sources.list.d/salt.list
+
+sudo apt-get -y update
+sudo apt-get -y install salt-minion
+sudo service salt-minion stop
+sudo systemctl disable salt-minion
+
+# Assumes the repository has already been cloned to the working directory
+# cd ~
+# git clone -b standalone https://github.com/Bioconductor/bioconductor_salt
+
+# Set up bioconductor's saltstack
+sudo cp -r bioconductor_salt/saltstack/salt /srv
+sudo cp -r bioconductor_salt/saltstack/pillar /srv
+sudo cp bioconductor_salt/saltstack/minion.d/minion.conf /etc/salt/minion
+
+sudo mv /srv/pillar/custom/release_standalone.sls /srv/pillar/custom/init.sls
+
+sudo salt-call --local state.highstate -l debug || true
+
+# Find R path and check that it works
+/home/biocbuild/bbs-*/R/bin/R --version > /tmp/rver
+if ! grep -q 'R version' /tmp/rver; then exit 1; fi
+
+RPATH="$(echo /home/biocbuild/bbs-*/R/bin)"
+
+echo "export PATH='$PATH:$RPATH'" | sudo tee -a /etc/profile
+echo "export PATH='$PATH:$RPATH'" | sudo tee -a /etc/bash.bashrc
+
+echo "#!/bin/bash" | sudo tee /bbs_r_start
+echo "$RPATH/R \"\$@\"" | sudo tee -a /bbs_r_start
+
+sudo chown biocbuild /bbs_r_start
+sudo chmod +x /bbs_r_start
+
+# Cleanup
+# rm -rf /srv /etc/salt
+# sudo apt-get -y purge salt-minion
+
+